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. 2016 Nov 10;59(21):9928-9941.
doi: 10.1021/acs.jmedchem.6b01315. Epub 2016 Oct 28.

Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable for Phase I Clinical Trials for B-Cell Lymphomas

Rishi G Vaswani  1 , Victor S Gehling  1 , Les A Dakin  1 , Andrew S Cook  1 , Christopher G Nasveschuk  1 , Martin Duplessis  1 , Priyadarshini Iyer  1 , Srividya Balasubramanian  1 , Feng Zhao  1 , Andrew C Good  1 , Robert Campbell  1 , Christina Lee  1 , Nico Cantone  1 , Richard T Cummings  1 , Emmanuel Normant  1 , Steven F Bellon  1 , Brian K Albrecht  1 , Jean-Christophe Harmange  1 , Patrick Trojer  1 , James E Audia  1 , Ying Zhang  1 , Neil Justin  1 , Shuyang Chen  1 , Jon R Wilson  1 , Steven J Gamblin  1
Affiliations

Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable for Phase I Clinical Trials for B-Cell Lymphomas

Rishi G Vaswani et al. J Med Chem. .

Abstract

Polycomb repressive complex 2 (PRC2) has been shown to play a major role in transcriptional silencing in part by installing methylation marks on lysine 27 of histone 3. Dysregulation of PRC2 function correlates with certain malignancies and poor prognosis. EZH2 is the catalytic engine of the PRC2 complex and thus represents a key candidate oncology target for pharmacological intervention. Here we report the optimization of our indole-based EZH2 inhibitor series that led to the identification of CPI-1205, a highly potent (biochemical IC50 = 0.002 μM, cellular EC50 = 0.032 μM) and selective inhibitor of EZH2. This compound demonstrates robust antitumor effects in a Karpas-422 xenograft model when dosed at 160 mg/kg BID and is currently in Phase I clinical trials. Additionally, we disclose the co-crystal structure of our inhibitor series bound to the human PRC2 complex.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Reported EZH2 inhibitors.
Figure 2
Figure 2
General trends in structure–activity relationships.
Figure 3
Figure 3
(A) Surface representation of the co-crystal structure of 10 (yellow spheres) bound to the PRC2 complex (EED (gray), SUZ12 (pink), EZH2 (pale blue at N-terminus to blue at C-terminus) (PDB ID: 5LS6). (B) Electron density (NCS averaged Fourier Map (2Fo-Fc map contoured at 2σ)) surrounding compound 10. Main interactions are between pyridone of 10 and key residues from the SET-I and SAL domains of EZH2 and from EED (PDB ID: 5LS6). (C) The PRC2-compound 10 complex (colored as above) superimposed on the PRC2 complex with SAH cofactor and peptide (green). (PDB ID: 5HYN). (D) The pyridone and indole are constrained in a binding site composed of residues from both the SET domain (blue) and SAL region (pale blue) of EZH2 (PDB ID: 5LS6).
Figure 4
Figure 4
Comparison of the EZH2 C-terminus with the SET domain active site. (A) Human PRC2 complex with compound 10. (PDB ID: 5LS6) (B) Equivalent region of the human PRC2-H3K27M-SAH complex, (PDB ID: 5HYN) with cofactor (orange) and histone H3 peptide (red). (C) Overlay of residues forming the SET domain lysine channel for both complexes, highlighting that the position of the C-terminus conformation observed in the compound complex is incompatible with substrate binding (red). (D) and (E) Surface representations showing that the lysine binding channel is closed in the PRC2-compound 10 complex (PDB ID: 5LS6) but accessible in the SAH/substrate complex (PDB ID: 5HYN). (F) Surface representation of EZH2 observed in the PRC2-compound 10 complex but with the H3 peptide overlaid from the PRC2-H3K27M-SAH complex, confirming that substrate binding is incompatible with the EZH2 conformation in the PRC2-compound 10 complex.
Figure 5
Figure 5
Mouse pharmacokinetic profile of 13.
Scheme 1
Scheme 1. Palladium Mediated Intramolecular C–N Arylation to Indole 14
Reagents and conditions: (a) AcOH, t-BuOH, reflux (76% yield); (b) RuPhos precatalyst (generation III) (2 mol %), RuPhos (3 mol %), NaOMe (1.5 equiv), 1,4-dioxane, 100 °C, followed by HCl (4 M in 1,4-dioxane) (81% yield over two steps).
Scheme 2
Scheme 2. Synthesis of 10 and 13
Reagents and conditions: (a) 2,2,2-trifluoroacetic anhydride (1.4 equiv), i-PrNEt2 (2.5 equiv), CH2Cl2, 0 °C; (b) BH3·THF (2.2 equiv), THF, 70 °C; (c) 6 N aq NaOH (6.0 equiv), EtOH, 85 °C; (d) CDI (1.3 equiv), THF, 60 °C
Figure 6
Figure 6
Tumor xenograft with 13. (A) Effect of dosing analogue 13 at 160 mpk BID for 25 days on KARPAS-422 tumor growth in mouse xenograft. (B) Corresponding body weight change during the course of the study. (C) Pharmacodynamic effect of 13 on reduction of H3K27me3 normalized to total H3. (D) Analysis of plasma and tumor concentrations of 13 at 1 h post last dose on day 25.
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